BORIS is a paralogue of CTCF, the global three-dimensional genome organizer. While CTCF is ubiquitously expressed, BORIS expression is restricted to germ and cancer cells, assigning BORIS as a cancer-testis gene. Our research of CTCF and BORIS is focused on developing appropriate tools to study functions of both factors. First, we generated knockout animals for the two factors and found that CTCF is essential for the very survival of the embryo, while BORIS is involved in normal spermatogenesis. BORIS-/- mice show a sub-fertility phenotype and multiple defects in spermatogenesis. Gene expression profiling of BORIS-/- mice uncovered the BORIS role in transcriptional activation of many testis-specific genes during spermatogenesis. In particular, expression of Gal3st1 and FerT testes-specific isoforms is induced by BORIS binding to intronic CTCF sites. Interestingly, both transcripts are products of genes that are male germ cell-specific homologs of genes expressed in somatic cells and both transcripts are aberrantly activated in cancer cells, coinciding with BORIS expression. To extend these two examples on a genome-wide level, we recently performed chromatin immunoprecipitation coupled with next generation sequencing (ChIP-Seq) to map both CTCF and BORIS sites in several cancer cell lines. Combining our ChIP-Seq, RNA-seq, and deep-CAGE-seq data with ENCODE next-generation data, we found that an aberrant expression of BORIS in cancer cells results in activation of multiple testis-specific genes from intronic CTCF binding sites. The interspecies conservation analysis of BORIS sites revealed the high conservation of over 80% of all sites between human and mice, allowing us to confirm a similar BORIS genome-wide occupancy in both human cancer cell lines and mouse round spermatids. Moreover, our data suggest that CTCF function is lost on some tumor-suppressor and oncogene promoters via BORIS recruitment and/or through BORIS and CTCF heterodimer formation at 2xCTSes binding sites. We also recently confirmed that intronic CTCF sites could be reprogrammed into alternative transcriptional start sites via BORIS occupancy through epigenetic remodeling of chromatin. To identify the molecular mechanisms by which BORIS activates the alternative transcription from intronic promoters, we plan to analyze what protein-partners are recruited by BORIS to initiate transcription and what kind of chromatin remodeling factors are involved in the activation of intronic class of Transcriptional Start Sites (TSSs) and whether any CTCF-assisted chromatin looping could be also involved by such TSS as well.